csd3
The system
1. System
2. Login
3. Directories
4. Policies
5. email
6. Languages
7. Software
8. Parallel Computing
8. ceuadmin
10. Green Algorithms
11. Training
12. Contacts
13. Acknowledgement
13. Appendix A. Setup of modules
/systems/files/
Python packages
1. gwas2vcf
2. GWAS Catalog
3. ldsc
4. PhySO
5. Scikit-LLM & OpenAI API
6. snakemake
7. Synapse
R packages
1. brms
2. conquer
3. DescTools
4. EasyQC
5. geometries
6. glmnet
7. gnn
8. gsl
9. igraph
10. jqr
11. LDlinkR
12. magick
13. METRO
14. nloptr
15. PhenoScanner
16. PKI
17. plumber
18. protolite
19. RcppTOML
20. Rfast
21. rgdal
22. rgeos
23. rgl
24. Rhdf5lib
25. rjags
26. rJava
27. RMariaDB
28. rstan
29. SAIGE
30. sf
31. snpnet
32. sojo
33. SPACox
34. tenXplore
35. xlsx
Applications
1. ABCtoolbox
2. AEGIS
3. akt
4. ANNOVAR
5. aria2
6. bcftools
7. bedops
8. bgenix
9. CaVEMaN
10. CAVIAR/eCAVIAR
11. circos
12. citeproc
13. CookHLA
14. Cytoscape
15. DNAnexus
16. DosageConverter
17. finemap
18. GATK
19. GCTA
20. geany
21. Genotype-Harmonizer
22. gsutil
23. hail
24. HESS
25. KentUtils
26. lapack
27. LEMMA
28. LocusZoom
29. METAL
30. MetaXcan
31. pandoc
32. PCA projection
33. peer
34. pgsc_calc
35. PLINK
36. polyphen-2
37. poppler
38. PRSice
39. PRSoS
40. pspp
41. AlphaPept and PyOpenMS
42. qpdf
43. qtltools
44. quarto
45. regenie
46. R
47. RStudio
48. Rust
49. shapeit
50. SMR
51. snipar
52. SNPTEST
53. sra-tools
54. SurvivalGWAS_SV
55. tabix
56. VEP
57. Visual Studio code
58. Appendix B. Notes on emsembl-vep
/applications/files/
/applications/files/examples/
cardio
csd3
systems
policies.md
Policies
See
https://docs.hpc.cam.ac.uk/hpc/user-guide/policies.html#acknowledging-csd3
.
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2019-2024,
cambridge-ceu
Revision
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